Setting up your development environment manually

In order to hack on SeqLike, you'll want to have your development environment set up. This document can serve as a tutorial document that shows you how to get setup.

Assumed knowledge

We'll throw this point out first: this is not really a beginner-friendly document. If you're here, we're assuming some knowledge:

You know about virtual environments and their flavours (venv, conda, etc.)
You're comfortable setting up virtual environments on your own.
The doc is conda-heavy, so familiarity with conda commands will be helpful.

There are usually multiple valid ways to set up an environment. If you're looking for a pretty fool-proof way to set up development environments without fiddling with all sorts of stuff, try out development containers.

Steps

tl;dr

Copy/paste this exactly only if you feel comfortable with the commands and know exactly what they're doing.

conda env create -f environment.yml
pip install -e .
pytest

Set up conda environment

We provide an environment.yml file that should get you started. Create the environment using the conda env create command:

conda env create -f environment.yml

Install the package in development mode

To hack on the package, and, more importantly, to run tests, you'll want to install SeqLike in development mode:

pip install -e .

Run tests

The surest way of knowing whether your environment is installed correctly is to run the test suite straight away. You can do this by running:

pytest

Build docs

This is another good way to test whether your environment is installed correctly or not.

mkdocs serve

You should be able to see the docs previewed at port 8000 on your localhost.

Update conda environment

If you ever need to update the environment, say, to obtain new package versions:

conda env update -f environment.yml